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comparison test-data/meme_output_test2.xml @ 2:b48e673af4e8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
author iuc
date Thu, 17 May 2018 14:11:15 -0400
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1:793225b11202 2:b48e673af4e8
1 <?xml version='1.0' encoding='UTF-8' standalone='yes'?>
2 <!-- Document definition -->
3 <!DOCTYPE MEME[
4 <!ELEMENT MEME (
5 training_set,
6 model,
7 motifs,
8 scanned_sites_summary?
9 )>
10 <!ATTLIST MEME
11 version CDATA #REQUIRED
12 release CDATA #REQUIRED
13 >
14 <!-- Training-set elements -->
15 <!ELEMENT training_set (alphabet, ambigs, sequence*, letter_frequencies)>
16 <!ATTLIST training_set datafile CDATA #REQUIRED length CDATA #REQUIRED>
17 <!ELEMENT alphabet (letter*)>
18 <!ATTLIST alphabet name CDATA #REQUIRED>
19 <!ELEMENT ambigs (letter*)>
20 <!ELEMENT letter EMPTY>
21 <!ATTLIST letter id ID #REQUIRED>
22 <!ATTLIST letter symbol CDATA #REQUIRED>
23 <!ATTLIST letter equals CDATA #IMPLIED>
24 <!ATTLIST letter aliases CDATA #IMPLIED>
25 <!ATTLIST letter complement CDATA #IMPLIED>
26 <!ATTLIST letter name CDATA #IMPLIED>
27 <!ATTLIST letter colour CDATA #IMPLIED>
28 <!ELEMENT sequence EMPTY>
29 <!ATTLIST sequence id ID #REQUIRED
30 name CDATA #REQUIRED
31 length CDATA #REQUIRED
32 weight CDATA #REQUIRED
33 >
34 <!ELEMENT letter_frequencies (alphabet_array)>
35
36 <!-- Model elements -->
37 <!ELEMENT model (
38 command_line,
39 host,
40 type,
41 nmotifs,
42 evalue_threshold,
43 object_function,
44 spfun,
45 min_width,
46 max_width,
47 wg,
48 ws,
49 endgaps,
50 minsites,
51 maxsites,
52 wnsites,
53 spmap,
54 spfuzz,
55 prior,
56 beta,
57 maxiter,
58 distance,
59 num_sequences,
60 num_positions,
61 seed,
62 hsfrac,
63 maxwords,
64 maxsize,
65 csites,
66 strands,
67 priors_file,
68 reason_for_stopping,
69 back_order,
70 background_frequencies
71 )>
72 <!ELEMENT command_line (#PCDATA)*>
73 <!ELEMENT host (#PCDATA)*>
74 <!ELEMENT type (#PCDATA)*>
75 <!ELEMENT nmotifs (#PCDATA)*>
76 <!ELEMENT evalue_threshold (#PCDATA)*>
77 <!ELEMENT object_function (#PCDATA)*>
78 <!ELEMENT spfun (#PCDATA)*>
79 <!ELEMENT min_width (#PCDATA)*>
80 <!ELEMENT max_width (#PCDATA)*>
81 <!ELEMENT wg (#PCDATA)*>
82 <!ELEMENT ws (#PCDATA)*>
83 <!ELEMENT endgaps (#PCDATA)*>
84 <!ELEMENT minsites (#PCDATA)*>
85 <!ELEMENT maxsites (#PCDATA)*>
86 <!ELEMENT wnsites (#PCDATA)*>
87 <!ELEMENT spmap (#PCDATA)*>
88 <!ELEMENT spfuzz (#PCDATA)*>
89 <!ELEMENT prior (#PCDATA)*>
90 <!ELEMENT beta (#PCDATA)*>
91 <!ELEMENT maxiter (#PCDATA)*>
92 <!ELEMENT distance (#PCDATA)*>
93 <!ELEMENT num_sequences (#PCDATA)*>
94 <!ELEMENT num_positions (#PCDATA)*>
95 <!ELEMENT seed (#PCDATA)*>
96 <!ELEMENT hsfrac (#PCDATA)*>
97 <!ELEMENT maxwords (#PCDATA)*>
98 <!ELEMENT maxsites (#PCDATA)*>
99 <!ELEMENT csites (#PCDATA)*>
100 <!ELEMENT strands (#PCDATA)*>
101 <!ELEMENT priors_file (#PCDATA)*>
102 <!ELEMENT reason_for_stopping (#PCDATA)*>
103 <!ELEMENT back_order (#PCDATA)*>
104 <!ELEMENT background_frequencies (alphabet_array)>
105 <!ATTLIST background_frequencies source CDATA #REQUIRED>
106
107 <!-- Motif elements -->
108 <!ELEMENT motifs (motif*)>
109 <!ELEMENT motif (scores, probabilities, regular_expression?, contributing_sites)>
110 <!ATTLIST motif id ID #REQUIRED
111 name CDATA #REQUIRED
112 alt CDATA ""
113 width CDATA #REQUIRED
114 sites CDATA #REQUIRED
115 llr CDATA #REQUIRED
116 ic CDATA #REQUIRED
117 re CDATA #REQUIRED
118 bayes_threshold CDATA #REQUIRED
119 e_value CDATA #REQUIRED
120 elapsed_time CDATA #REQUIRED
121 url CDATA ""
122 >
123 <!ELEMENT scores (alphabet_matrix)>
124 <!ELEMENT probabilities (alphabet_matrix)>
125 <!ELEMENT regular_expression (#PCDATA)*>
126
127 <!-- Contributing site elements -->
128 <!-- Contributing sites are motif occurences found during the motif discovery phase -->
129 <!ELEMENT contributing_sites (contributing_site*)>
130 <!ELEMENT contributing_site (left_flank, site, right_flank)>
131 <!ATTLIST contributing_site sequence_id IDREF #REQUIRED
132 position CDATA #REQUIRED
133 strand (plus|minus|none) 'none'
134 pvalue CDATA #REQUIRED
135 >
136 <!-- The left_flank contains the sequence for 10 bases to the left of the motif start -->
137 <!ELEMENT left_flank (#PCDATA)>
138 <!-- The site contains the sequence for the motif instance -->
139 <!ELEMENT site (letter_ref*)>
140 <!-- The right_flank contains the sequence for 10 bases to the right of the motif end -->
141 <!ELEMENT right_flank (#PCDATA)>
142
143 <!-- Scanned site elements -->
144 <!-- Scanned sites are motif occurences found during the sequence scan phase -->
145 <!ELEMENT scanned_sites_summary (scanned_sites*)>
146 <!ATTLIST scanned_sites_summary p_thresh CDATA #REQUIRED>
147 <!ELEMENT scanned_sites (scanned_site*)>
148 <!ATTLIST scanned_sites sequence_id IDREF #REQUIRED
149 pvalue CDATA #REQUIRED
150 num_sites CDATA #REQUIRED>
151 <!ELEMENT scanned_site EMPTY>
152 <!ATTLIST scanned_site motif_id IDREF #REQUIRED
153 strand (plus|minus|none) 'none'
154 position CDATA #REQUIRED
155 pvalue CDATA #REQUIRED>
156
157 <!-- Utility elements -->
158 <!-- A reference to a letter in the alphabet -->
159 <!ELEMENT letter_ref EMPTY>
160 <!ATTLIST letter_ref letter_id IDREF #REQUIRED>
161 <!-- A alphabet-array contains one floating point value for each letter in an alphabet -->
162 <!ELEMENT alphabet_array (value*)>
163 <!ELEMENT value (#PCDATA)>
164 <!ATTLIST value letter_id IDREF #REQUIRED>
165
166 <!-- A alphabet_matrix contains one alphabet_array for each position in a motif -->
167 <!ELEMENT alphabet_matrix (alphabet_array*)>
168
169 ]>
170 <!-- Begin document body -->
171 <MEME version="4.12.0" release="Tue Jun 27 16:22:50 2017 -0700">
172 <training_set datafile="Galaxy_FASTA_Input" length="30">
173 <alphabet name="DNA" like="dna">
174 <letter id="A" symbol="A" complement="T" name="Adenine" colour="CC0000"/>
175 <letter id="C" symbol="C" complement="G" name="Cytosine" colour="0000CC"/>
176 <letter id="G" symbol="G" complement="C" name="Guanine" colour="FFB300"/>
177 <letter id="T" symbol="T" aliases="U" complement="A" name="Thymine" colour="008000"/>
178 <letter id="N" symbol="N" aliases="X." equals="ACGT" name="Any base"/>
179 <letter id="V" symbol="V" equals="ACG" name="Not T"/>
180 <letter id="H" symbol="H" equals="ACT" name="Not G"/>
181 <letter id="D" symbol="D" equals="AGT" name="Not C"/>
182 <letter id="B" symbol="B" equals="CGT" name="Not A"/>
183 <letter id="M" symbol="M" equals="AC" name="Amino"/>
184 <letter id="R" symbol="R" equals="AG" name="Purine"/>
185 <letter id="W" symbol="W" equals="AT" name="Weak"/>
186 <letter id="S" symbol="S" equals="CG" name="Strong"/>
187 <letter id="Y" symbol="Y" equals="CT" name="Pyrimidine"/>
188 <letter id="K" symbol="K" equals="GT" name="Keto"/>
189 </alphabet>
190 <sequence id="sequence_0" name="chr21_19617074_19617124_+" length="50" weight="1.000000" />
191 <sequence id="sequence_1" name="chr21_26934381_26934431_+" length="50" weight="1.000000" />
192 <sequence id="sequence_2" name="chr21_28217753_28217803_-" length="50" weight="1.000000" />
193 <sequence id="sequence_3" name="chr21_31710037_31710087_-" length="50" weight="1.000000" />
194 <sequence id="sequence_4" name="chr21_31744582_31744632_-" length="50" weight="1.000000" />
195 <sequence id="sequence_5" name="chr21_31768316_31768366_+" length="50" weight="1.000000" />
196 <sequence id="sequence_6" name="chr21_31914206_31914256_-" length="50" weight="1.000000" />
197 <sequence id="sequence_7" name="chr21_31933633_31933683_-" length="50" weight="1.000000" />
198 <sequence id="sequence_8" name="chr21_31962741_31962791_-" length="50" weight="1.000000" />
199 <sequence id="sequence_9" name="chr21_31964683_31964733_+" length="50" weight="1.000000" />
200 <sequence id="sequence_10" name="chr21_31973364_31973414_+" length="50" weight="1.000000" />
201 <sequence id="sequence_11" name="chr21_31992870_31992920_+" length="50" weight="1.000000" />
202 <sequence id="sequence_12" name="chr21_32185595_32185645_-" length="50" weight="1.000000" />
203 <sequence id="sequence_13" name="chr21_32202076_32202126_-" length="50" weight="1.000000" />
204 <sequence id="sequence_14" name="chr21_32253899_32253949_-" length="50" weight="1.000000" />
205 <sequence id="sequence_15" name="chr21_32410820_32410870_-" length="50" weight="1.000000" />
206 <sequence id="sequence_16" name="chr21_36411748_36411798_-" length="50" weight="1.000000" />
207 <sequence id="sequence_17" name="chr21_37838750_37838800_-" length="50" weight="1.000000" />
208 <sequence id="sequence_18" name="chr21_45705687_45705737_+" length="50" weight="1.000000" />
209 <sequence id="sequence_19" name="chr21_45971413_45971463_-" length="50" weight="1.000000" />
210 <sequence id="sequence_20" name="chr21_45978668_45978718_-" length="50" weight="1.000000" />
211 <sequence id="sequence_21" name="chr21_45993530_45993580_+" length="50" weight="1.000000" />
212 <sequence id="sequence_22" name="chr21_46020421_46020471_+" length="50" weight="1.000000" />
213 <sequence id="sequence_23" name="chr21_46031920_46031970_+" length="50" weight="1.000000" />
214 <sequence id="sequence_24" name="chr21_46046964_46047014_+" length="50" weight="1.000000" />
215 <sequence id="sequence_25" name="chr21_46057197_46057247_+" length="50" weight="1.000000" />
216 <sequence id="sequence_26" name="chr21_46086869_46086919_-" length="50" weight="1.000000" />
217 <sequence id="sequence_27" name="chr21_46102103_46102153_-" length="50" weight="1.000000" />
218 <sequence id="sequence_28" name="chr21_47517957_47518007_+" length="50" weight="1.000000" />
219 <sequence id="sequence_29" name="chr21_47575506_47575556_-" length="50" weight="1.000000" />
220 <letter_frequencies>
221 <alphabet_array>
222 <value letter_id="A">0.294</value>
223 <value letter_id="C">0.231</value>
224 <value letter_id="G">0.257</value>
225 <value letter_id="T">0.217</value>
226 </alphabet_array>
227 </letter_frequencies>
228 </training_set>
229 <model>
230 <command_line>meme meme_input_1.fasta -o meme_test2_out -nostatus -maxsize 1000000 -sf Galaxy_FASTA_Input -dna -mod zoops -nmotifs 1 -wnsites 0.8 -minw 8 -maxw 50 -wg 11 -ws 1 -maxiter 50 -distance 0.001 -prior dirichlet -b 0.01 -plib prior30.plib -spmap uni -spfuzz 0.5 </command_line>
231 <host>ThinkPad-T450s</host>
232 <type>zoops</type>
233 <nmotifs>1</nmotifs>
234 <evalue_threshold>inf</evalue_threshold>
235 <object_function>E-value of product of p-values</object_function>
236 <use_llr>0</use_llr>
237 <min_width>8</min_width>
238 <max_width>50</max_width>
239 <wg>11</wg>
240 <ws>1</ws>
241 <endgaps>yes</endgaps>
242 <substring>yes</substring>
243 <minsites>2</minsites>
244 <maxsites>30</maxsites>
245 <wnsites>0.8</wnsites>
246 <spmap>uni</spmap>
247 <spfuzz>0.5</spfuzz>
248 <prior>dirichlet</prior>
249 <beta>0.01</beta>
250 <maxiter>50</maxiter>
251 <distance>0.001</distance>
252 <num_sequences>30</num_sequences>
253 <num_positions>1500</num_positions>
254 <seed>0</seed>
255 <ctfrac>-1</ctfrac>
256 <maxwords>-1</maxwords>
257 <strands>forward</strands>
258 <priors_file>prior30.plib</priors_file>
259 <reason_for_stopping>Stopped because requested number of motifs (1) found.</reason_for_stopping>
260 <background_frequencies source="dataset with add-one prior applied">
261 <alphabet_array>
262 <value letter_id="A">0.294</value>
263 <value letter_id="C">0.231</value>
264 <value letter_id="G">0.257</value>
265 <value letter_id="T">0.217</value>
266 </alphabet_array>
267 </background_frequencies>
268 </model>
269 <motifs>
270 <motif id="motif_1" name="GGSRTATAAAA" alt="MEME-1" width="11" sites="30" ic="13.0" re="12.2" llr="254" e_value="5.1e-040" bayes_threshold="5.2854" elapsed_time="0.376000">
271 <scores>
272 <alphabet_matrix>
273 <alphabet_array>
274 <value letter_id="A">-14</value>
275 <value letter_id="C">-179</value>
276 <value letter_id="G">114</value>
277 <value letter_id="T">-112</value>
278 </alphabet_array>
279 <alphabet_array>
280 <value letter_id="A">3</value>
281 <value letter_id="C">-1155</value>
282 <value letter_id="G">137</value>
283 <value letter_id="T">-270</value>
284 </alphabet_array>
285 <alphabet_array>
286 <value letter_id="A">-114</value>
287 <value letter_id="C">20</value>
288 <value letter_id="G">86</value>
289 <value letter_id="T">-71</value>
290 </alphabet_array>
291 <alphabet_array>
292 <value letter_id="A">3</value>
293 <value letter_id="C">-279</value>
294 <value letter_id="G">122</value>
295 <value letter_id="T">-170</value>
296 </alphabet_array>
297 <alphabet_array>
298 <value letter_id="A">-1155</value>
299 <value letter_id="C">-1155</value>
300 <value letter_id="G">-295</value>
301 <value letter_id="T">215</value>
302 </alphabet_array>
303 <alphabet_array>
304 <value letter_id="A">156</value>
305 <value letter_id="C">-179</value>
306 <value letter_id="G">-1155</value>
307 <value letter_id="T">-170</value>
308 </alphabet_array>
309 <alphabet_array>
310 <value letter_id="A">-1155</value>
311 <value letter_id="C">-1155</value>
312 <value letter_id="G">-1155</value>
313 <value letter_id="T">220</value>
314 </alphabet_array>
315 <alphabet_array>
316 <value letter_id="A">172</value>
317 <value letter_id="C">-279</value>
318 <value letter_id="G">-1155</value>
319 <value letter_id="T">-1155</value>
320 </alphabet_array>
321 <alphabet_array>
322 <value letter_id="A">125</value>
323 <value letter_id="C">-1155</value>
324 <value letter_id="G">-1155</value>
325 <value letter_id="T">46</value>
326 </alphabet_array>
327 <alphabet_array>
328 <value letter_id="A">167</value>
329 <value letter_id="C">-179</value>
330 <value letter_id="G">-1155</value>
331 <value letter_id="T">-1155</value>
332 </alphabet_array>
333 <alphabet_array>
334 <value letter_id="A">144</value>
335 <value letter_id="C">-1155</value>
336 <value letter_id="G">-63</value>
337 <value letter_id="T">-270</value>
338 </alphabet_array>
339 </alphabet_matrix>
340 </scores>
341 <probabilities>
342 <alphabet_matrix>
343 <alphabet_array>
344 <value letter_id="A">0.266667</value>
345 <value letter_id="C">0.066667</value>
346 <value letter_id="G">0.566667</value>
347 <value letter_id="T">0.100000</value>
348 </alphabet_array>
349 <alphabet_array>
350 <value letter_id="A">0.300000</value>
351 <value letter_id="C">0.000000</value>
352 <value letter_id="G">0.666667</value>
353 <value letter_id="T">0.033333</value>
354 </alphabet_array>
355 <alphabet_array>
356 <value letter_id="A">0.133333</value>
357 <value letter_id="C">0.266667</value>
358 <value letter_id="G">0.466667</value>
359 <value letter_id="T">0.133333</value>
360 </alphabet_array>
361 <alphabet_array>
362 <value letter_id="A">0.300000</value>
363 <value letter_id="C">0.033333</value>
364 <value letter_id="G">0.600000</value>
365 <value letter_id="T">0.066667</value>
366 </alphabet_array>
367 <alphabet_array>
368 <value letter_id="A">0.000000</value>
369 <value letter_id="C">0.000000</value>
370 <value letter_id="G">0.033333</value>
371 <value letter_id="T">0.966667</value>
372 </alphabet_array>
373 <alphabet_array>
374 <value letter_id="A">0.866667</value>
375 <value letter_id="C">0.066667</value>
376 <value letter_id="G">0.000000</value>
377 <value letter_id="T">0.066667</value>
378 </alphabet_array>
379 <alphabet_array>
380 <value letter_id="A">0.000000</value>
381 <value letter_id="C">0.000000</value>
382 <value letter_id="G">0.000000</value>
383 <value letter_id="T">1.000000</value>
384 </alphabet_array>
385 <alphabet_array>
386 <value letter_id="A">0.966667</value>
387 <value letter_id="C">0.033333</value>
388 <value letter_id="G">0.000000</value>
389 <value letter_id="T">0.000000</value>
390 </alphabet_array>
391 <alphabet_array>
392 <value letter_id="A">0.700000</value>
393 <value letter_id="C">0.000000</value>
394 <value letter_id="G">0.000000</value>
395 <value letter_id="T">0.300000</value>
396 </alphabet_array>
397 <alphabet_array>
398 <value letter_id="A">0.933333</value>
399 <value letter_id="C">0.066667</value>
400 <value letter_id="G">0.000000</value>
401 <value letter_id="T">0.000000</value>
402 </alphabet_array>
403 <alphabet_array>
404 <value letter_id="A">0.800000</value>
405 <value letter_id="C">0.000000</value>
406 <value letter_id="G">0.166667</value>
407 <value letter_id="T">0.033333</value>
408 </alphabet_array>
409 </alphabet_matrix>
410 </probabilities>
411 <regular_expression>
412 [GA][GA][GC][GA]TATA[AT]AA
413 </regular_expression>
414 <contributing_sites>
415 <contributing_site sequence_id="sequence_24" position="12" strand="plus" pvalue="4.51e-07" >
416 <left_flank>AAGGCCAGGA</left_flank>
417 <site>
418 <letter_ref letter_id="G"/>
419 <letter_ref letter_id="G"/>
420 <letter_ref letter_id="G"/>
421 <letter_ref letter_id="G"/>
422 <letter_ref letter_id="T"/>
423 <letter_ref letter_id="A"/>
424 <letter_ref letter_id="T"/>
425 <letter_ref letter_id="A"/>
426 <letter_ref letter_id="A"/>
427 <letter_ref letter_id="A"/>
428 <letter_ref letter_id="A"/>
429 </site>
430 <right_flank>GCCTGAGAGC</right_flank>
431 </contributing_site>
432 <contributing_site sequence_id="sequence_23" position="15" strand="plus" pvalue="2.22e-06" >
433 <left_flank>ATACCCAGGG</left_flank>
434 <site>
435 <letter_ref letter_id="A"/>
436 <letter_ref letter_id="G"/>
437 <letter_ref letter_id="G"/>
438 <letter_ref letter_id="G"/>
439 <letter_ref letter_id="T"/>
440 <letter_ref letter_id="A"/>
441 <letter_ref letter_id="T"/>
442 <letter_ref letter_id="A"/>
443 <letter_ref letter_id="A"/>
444 <letter_ref letter_id="A"/>
445 <letter_ref letter_id="A"/>
446 </site>
447 <right_flank>CCTCAGCAGC</right_flank>
448 </contributing_site>
449 <contributing_site sequence_id="sequence_13" position="13" strand="plus" pvalue="2.74e-06" >
450 <left_flank>CCACCAGCTT</left_flank>
451 <site>
452 <letter_ref letter_id="G"/>
453 <letter_ref letter_id="A"/>
454 <letter_ref letter_id="G"/>
455 <letter_ref letter_id="G"/>
456 <letter_ref letter_id="T"/>
457 <letter_ref letter_id="A"/>
458 <letter_ref letter_id="T"/>
459 <letter_ref letter_id="A"/>
460 <letter_ref letter_id="A"/>
461 <letter_ref letter_id="A"/>
462 <letter_ref letter_id="A"/>
463 </site>
464 <right_flank>AGCCCTGTAC</right_flank>
465 </contributing_site>
466 <contributing_site sequence_id="sequence_25" position="36" strand="plus" pvalue="4.86e-06" >
467 <left_flank>ACAGGCCCTG</left_flank>
468 <site>
469 <letter_ref letter_id="G"/>
470 <letter_ref letter_id="G"/>
471 <letter_ref letter_id="C"/>
472 <letter_ref letter_id="A"/>
473 <letter_ref letter_id="T"/>
474 <letter_ref letter_id="A"/>
475 <letter_ref letter_id="T"/>
476 <letter_ref letter_id="A"/>
477 <letter_ref letter_id="A"/>
478 <letter_ref letter_id="A"/>
479 <letter_ref letter_id="A"/>
480 </site>
481 <right_flank>GCC</right_flank>
482 </contributing_site>
483 <contributing_site sequence_id="sequence_21" position="7" strand="plus" pvalue="4.86e-06" >
484 <left_flank>CCAAGGA</left_flank>
485 <site>
486 <letter_ref letter_id="G"/>
487 <letter_ref letter_id="G"/>
488 <letter_ref letter_id="A"/>
489 <letter_ref letter_id="G"/>
490 <letter_ref letter_id="T"/>
491 <letter_ref letter_id="A"/>
492 <letter_ref letter_id="T"/>
493 <letter_ref letter_id="A"/>
494 <letter_ref letter_id="A"/>
495 <letter_ref letter_id="A"/>
496 <letter_ref letter_id="A"/>
497 </site>
498 <right_flank>GCCCCACAAA</right_flank>
499 </contributing_site>
500 <contributing_site sequence_id="sequence_19" position="9" strand="plus" pvalue="4.86e-06" >
501 <left_flank>CAGGCCCTG</left_flank>
502 <site>
503 <letter_ref letter_id="G"/>
504 <letter_ref letter_id="G"/>
505 <letter_ref letter_id="C"/>
506 <letter_ref letter_id="A"/>
507 <letter_ref letter_id="T"/>
508 <letter_ref letter_id="A"/>
509 <letter_ref letter_id="T"/>
510 <letter_ref letter_id="A"/>
511 <letter_ref letter_id="A"/>
512 <letter_ref letter_id="A"/>
513 <letter_ref letter_id="A"/>
514 </site>
515 <right_flank>GCCCCAGCAG</right_flank>
516 </contributing_site>
517 <contributing_site sequence_id="sequence_9" position="13" strand="plus" pvalue="4.86e-06" >
518 <left_flank>GATTCACTGA</left_flank>
519 <site>
520 <letter_ref letter_id="G"/>
521 <letter_ref letter_id="G"/>
522 <letter_ref letter_id="C"/>
523 <letter_ref letter_id="A"/>
524 <letter_ref letter_id="T"/>
525 <letter_ref letter_id="A"/>
526 <letter_ref letter_id="T"/>
527 <letter_ref letter_id="A"/>
528 <letter_ref letter_id="A"/>
529 <letter_ref letter_id="A"/>
530 <letter_ref letter_id="A"/>
531 </site>
532 <right_flank>GGCCCTCTGC</right_flank>
533 </contributing_site>
534 <contributing_site sequence_id="sequence_28" position="32" strand="plus" pvalue="6.48e-06" >
535 <left_flank>CCGGCGGGGC</left_flank>
536 <site>
537 <letter_ref letter_id="G"/>
538 <letter_ref letter_id="G"/>
539 <letter_ref letter_id="G"/>
540 <letter_ref letter_id="G"/>
541 <letter_ref letter_id="T"/>
542 <letter_ref letter_id="A"/>
543 <letter_ref letter_id="T"/>
544 <letter_ref letter_id="A"/>
545 <letter_ref letter_id="A"/>
546 <letter_ref letter_id="A"/>
547 <letter_ref letter_id="G"/>
548 </site>
549 <right_flank>GGGGCGG</right_flank>
550 </contributing_site>
551 <contributing_site sequence_id="sequence_20" position="4" strand="plus" pvalue="6.48e-06" >
552 <left_flank>CAGA</left_flank>
553 <site>
554 <letter_ref letter_id="G"/>
555 <letter_ref letter_id="G"/>
556 <letter_ref letter_id="G"/>
557 <letter_ref letter_id="G"/>
558 <letter_ref letter_id="T"/>
559 <letter_ref letter_id="A"/>
560 <letter_ref letter_id="T"/>
561 <letter_ref letter_id="A"/>
562 <letter_ref letter_id="A"/>
563 <letter_ref letter_id="A"/>
564 <letter_ref letter_id="G"/>
565 </site>
566 <right_flank>GTTCCGACCA</right_flank>
567 </contributing_site>
568 <contributing_site sequence_id="sequence_12" position="18" strand="plus" pvalue="6.48e-06" >
569 <left_flank>CACCAGAGCT</left_flank>
570 <site>
571 <letter_ref letter_id="G"/>
572 <letter_ref letter_id="G"/>
573 <letter_ref letter_id="G"/>
574 <letter_ref letter_id="A"/>
575 <letter_ref letter_id="T"/>
576 <letter_ref letter_id="A"/>
577 <letter_ref letter_id="T"/>
578 <letter_ref letter_id="A"/>
579 <letter_ref letter_id="T"/>
580 <letter_ref letter_id="A"/>
581 <letter_ref letter_id="A"/>
582 </site>
583 <right_flank>AGAAGGTTCT</right_flank>
584 </contributing_site>
585 <contributing_site sequence_id="sequence_15" position="21" strand="plus" pvalue="1.38e-05" >
586 <left_flank>AATCACTGAG</left_flank>
587 <site>
588 <letter_ref letter_id="G"/>
589 <letter_ref letter_id="A"/>
590 <letter_ref letter_id="T"/>
591 <letter_ref letter_id="G"/>
592 <letter_ref letter_id="T"/>
593 <letter_ref letter_id="A"/>
594 <letter_ref letter_id="T"/>
595 <letter_ref letter_id="A"/>
596 <letter_ref letter_id="A"/>
597 <letter_ref letter_id="A"/>
598 <letter_ref letter_id="A"/>
599 </site>
600 <right_flank>GTCCCAGGGA</right_flank>
601 </contributing_site>
602 <contributing_site sequence_id="sequence_11" position="16" strand="plus" pvalue="1.38e-05" >
603 <left_flank>CACTATTGAA</left_flank>
604 <site>
605 <letter_ref letter_id="G"/>
606 <letter_ref letter_id="A"/>
607 <letter_ref letter_id="T"/>
608 <letter_ref letter_id="G"/>
609 <letter_ref letter_id="T"/>
610 <letter_ref letter_id="A"/>
611 <letter_ref letter_id="T"/>
612 <letter_ref letter_id="A"/>
613 <letter_ref letter_id="A"/>
614 <letter_ref letter_id="A"/>
615 <letter_ref letter_id="A"/>
616 </site>
617 <right_flank>TTTCATTTGC</right_flank>
618 </contributing_site>
619 <contributing_site sequence_id="sequence_0" position="39" strand="plus" pvalue="1.41e-05" >
620 <left_flank>CCTCGGGACG</left_flank>
621 <site>
622 <letter_ref letter_id="T"/>
623 <letter_ref letter_id="G"/>
624 <letter_ref letter_id="G"/>
625 <letter_ref letter_id="G"/>
626 <letter_ref letter_id="T"/>
627 <letter_ref letter_id="A"/>
628 <letter_ref letter_id="T"/>
629 <letter_ref letter_id="A"/>
630 <letter_ref letter_id="T"/>
631 <letter_ref letter_id="A"/>
632 <letter_ref letter_id="A"/>
633 </site>
634 <right_flank></right_flank>
635 </contributing_site>
636 <contributing_site sequence_id="sequence_6" position="15" strand="plus" pvalue="1.61e-05" >
637 <left_flank>CCCACTACTT</left_flank>
638 <site>
639 <letter_ref letter_id="A"/>
640 <letter_ref letter_id="G"/>
641 <letter_ref letter_id="A"/>
642 <letter_ref letter_id="G"/>
643 <letter_ref letter_id="T"/>
644 <letter_ref letter_id="A"/>
645 <letter_ref letter_id="T"/>
646 <letter_ref letter_id="A"/>
647 <letter_ref letter_id="A"/>
648 <letter_ref letter_id="A"/>
649 <letter_ref letter_id="A"/>
650 </site>
651 <right_flank>TCATTCTGAG</right_flank>
652 </contributing_site>
653 <contributing_site sequence_id="sequence_22" position="2" strand="plus" pvalue="1.95e-05" >
654 <left_flank>GA</left_flank>
655 <site>
656 <letter_ref letter_id="G"/>
657 <letter_ref letter_id="A"/>
658 <letter_ref letter_id="C"/>
659 <letter_ref letter_id="A"/>
660 <letter_ref letter_id="T"/>
661 <letter_ref letter_id="A"/>
662 <letter_ref letter_id="T"/>
663 <letter_ref letter_id="A"/>
664 <letter_ref letter_id="A"/>
665 <letter_ref letter_id="A"/>
666 <letter_ref letter_id="A"/>
667 </site>
668 <right_flank>GCCAACATCC</right_flank>
669 </contributing_site>
670 <contributing_site sequence_id="sequence_14" position="17" strand="plus" pvalue="1.95e-05" >
671 <left_flank>CCCACCAGCA</left_flank>
672 <site>
673 <letter_ref letter_id="A"/>
674 <letter_ref letter_id="G"/>
675 <letter_ref letter_id="G"/>
676 <letter_ref letter_id="A"/>
677 <letter_ref letter_id="T"/>
678 <letter_ref letter_id="A"/>
679 <letter_ref letter_id="T"/>
680 <letter_ref letter_id="A"/>
681 <letter_ref letter_id="T"/>
682 <letter_ref letter_id="A"/>
683 <letter_ref letter_id="A"/>
684 </site>
685 <right_flank>AAGCTCAGGA</right_flank>
686 </contributing_site>
687 <contributing_site sequence_id="sequence_18" position="37" strand="plus" pvalue="2.16e-05" >
688 <left_flank>CGTGGTCGCG</left_flank>
689 <site>
690 <letter_ref letter_id="G"/>
691 <letter_ref letter_id="G"/>
692 <letter_ref letter_id="G"/>
693 <letter_ref letter_id="G"/>
694 <letter_ref letter_id="T"/>
695 <letter_ref letter_id="A"/>
696 <letter_ref letter_id="T"/>
697 <letter_ref letter_id="A"/>
698 <letter_ref letter_id="A"/>
699 <letter_ref letter_id="C"/>
700 <letter_ref letter_id="A"/>
701 </site>
702 <right_flank>GC</right_flank>
703 </contributing_site>
704 <contributing_site sequence_id="sequence_29" position="30" strand="plus" pvalue="3.04e-05" >
705 <left_flank>GCTGCCGGTG</left_flank>
706 <site>
707 <letter_ref letter_id="A"/>
708 <letter_ref letter_id="G"/>
709 <letter_ref letter_id="C"/>
710 <letter_ref letter_id="G"/>
711 <letter_ref letter_id="T"/>
712 <letter_ref letter_id="A"/>
713 <letter_ref letter_id="T"/>
714 <letter_ref letter_id="A"/>
715 <letter_ref letter_id="A"/>
716 <letter_ref letter_id="A"/>
717 <letter_ref letter_id="G"/>
718 </site>
719 <right_flank>GCCCTGGCG</right_flank>
720 </contributing_site>
721 <contributing_site sequence_id="sequence_4" position="12" strand="plus" pvalue="3.04e-05" >
722 <left_flank>CAGGTCTAAG</left_flank>
723 <site>
724 <letter_ref letter_id="A"/>
725 <letter_ref letter_id="G"/>
726 <letter_ref letter_id="C"/>
727 <letter_ref letter_id="A"/>
728 <letter_ref letter_id="T"/>
729 <letter_ref letter_id="A"/>
730 <letter_ref letter_id="T"/>
731 <letter_ref letter_id="A"/>
732 <letter_ref letter_id="T"/>
733 <letter_ref letter_id="A"/>
734 <letter_ref letter_id="A"/>
735 </site>
736 <right_flank>CTTGGAGTCC</right_flank>
737 </contributing_site>
738 <contributing_site sequence_id="sequence_5" position="0" strand="plus" pvalue="3.67e-05" >
739 <left_flank></left_flank>
740 <site>
741 <letter_ref letter_id="A"/>
742 <letter_ref letter_id="A"/>
743 <letter_ref letter_id="C"/>
744 <letter_ref letter_id="G"/>
745 <letter_ref letter_id="T"/>
746 <letter_ref letter_id="A"/>
747 <letter_ref letter_id="T"/>
748 <letter_ref letter_id="A"/>
749 <letter_ref letter_id="T"/>
750 <letter_ref letter_id="A"/>
751 <letter_ref letter_id="A"/>
752 </site>
753 <right_flank>ATGGTCCTGT</right_flank>
754 </contributing_site>
755 <contributing_site sequence_id="sequence_1" position="27" strand="plus" pvalue="3.93e-05" >
756 <left_flank>AGTCACAAGT</left_flank>
757 <site>
758 <letter_ref letter_id="G"/>
759 <letter_ref letter_id="A"/>
760 <letter_ref letter_id="G"/>
761 <letter_ref letter_id="T"/>
762 <letter_ref letter_id="T"/>
763 <letter_ref letter_id="A"/>
764 <letter_ref letter_id="T"/>
765 <letter_ref letter_id="A"/>
766 <letter_ref letter_id="A"/>
767 <letter_ref letter_id="A"/>
768 <letter_ref letter_id="A"/>
769 </site>
770 <right_flank>GGGTCGCACG</right_flank>
771 </contributing_site>
772 <contributing_site sequence_id="sequence_7" position="4" strand="plus" pvalue="5.65e-05" >
773 <left_flank>TCAG</left_flank>
774 <site>
775 <letter_ref letter_id="A"/>
776 <letter_ref letter_id="G"/>
777 <letter_ref letter_id="T"/>
778 <letter_ref letter_id="A"/>
779 <letter_ref letter_id="T"/>
780 <letter_ref letter_id="A"/>
781 <letter_ref letter_id="T"/>
782 <letter_ref letter_id="A"/>
783 <letter_ref letter_id="T"/>
784 <letter_ref letter_id="A"/>
785 <letter_ref letter_id="A"/>
786 </site>
787 <right_flank>ATGTTCCTGT</right_flank>
788 </contributing_site>
789 <contributing_site sequence_id="sequence_3" position="14" strand="plus" pvalue="6.24e-05" >
790 <left_flank>CCCAGGTTTC</left_flank>
791 <site>
792 <letter_ref letter_id="T"/>
793 <letter_ref letter_id="G"/>
794 <letter_ref letter_id="A"/>
795 <letter_ref letter_id="G"/>
796 <letter_ref letter_id="T"/>
797 <letter_ref letter_id="A"/>
798 <letter_ref letter_id="T"/>
799 <letter_ref letter_id="A"/>
800 <letter_ref letter_id="T"/>
801 <letter_ref letter_id="A"/>
802 <letter_ref letter_id="A"/>
803 </site>
804 <right_flank>TCGCCGCACC</right_flank>
805 </contributing_site>
806 <contributing_site sequence_id="sequence_16" position="22" strand="plus" pvalue="7.15e-05" >
807 <left_flank>AGTTTCAGTT</left_flank>
808 <site>
809 <letter_ref letter_id="G"/>
810 <letter_ref letter_id="G"/>
811 <letter_ref letter_id="C"/>
812 <letter_ref letter_id="A"/>
813 <letter_ref letter_id="T"/>
814 <letter_ref letter_id="C"/>
815 <letter_ref letter_id="T"/>
816 <letter_ref letter_id="A"/>
817 <letter_ref letter_id="A"/>
818 <letter_ref letter_id="A"/>
819 <letter_ref letter_id="A"/>
820 </site>
821 <right_flank>attatataac</right_flank>
822 </contributing_site>
823 <contributing_site sequence_id="sequence_27" position="36" strand="plus" pvalue="1.39e-04" >
824 <left_flank>TGCCTGGGTC</left_flank>
825 <site>
826 <letter_ref letter_id="C"/>
827 <letter_ref letter_id="A"/>
828 <letter_ref letter_id="G"/>
829 <letter_ref letter_id="G"/>
830 <letter_ref letter_id="T"/>
831 <letter_ref letter_id="A"/>
832 <letter_ref letter_id="T"/>
833 <letter_ref letter_id="A"/>
834 <letter_ref letter_id="A"/>
835 <letter_ref letter_id="A"/>
836 <letter_ref letter_id="G"/>
837 </site>
838 <right_flank>GCT</right_flank>
839 </contributing_site>
840 <contributing_site sequence_id="sequence_26" position="37" strand="plus" pvalue="1.39e-04" >
841 <left_flank>TGCCTGGGCC</left_flank>
842 <site>
843 <letter_ref letter_id="C"/>
844 <letter_ref letter_id="A"/>
845 <letter_ref letter_id="G"/>
846 <letter_ref letter_id="G"/>
847 <letter_ref letter_id="T"/>
848 <letter_ref letter_id="A"/>
849 <letter_ref letter_id="T"/>
850 <letter_ref letter_id="A"/>
851 <letter_ref letter_id="A"/>
852 <letter_ref letter_id="A"/>
853 <letter_ref letter_id="G"/>
854 </site>
855 <right_flank>GC</right_flank>
856 </contributing_site>
857 <contributing_site sequence_id="sequence_17" position="2" strand="plus" pvalue="4.81e-04" >
858 <left_flank>ga</left_flank>
859 <site>
860 <letter_ref letter_id="T"/>
861 <letter_ref letter_id="G"/>
862 <letter_ref letter_id="G"/>
863 <letter_ref letter_id="T"/>
864 <letter_ref letter_id="T"/>
865 <letter_ref letter_id="T"/>
866 <letter_ref letter_id="T"/>
867 <letter_ref letter_id="A"/>
868 <letter_ref letter_id="T"/>
869 <letter_ref letter_id="A"/>
870 <letter_ref letter_id="A"/>
871 </site>
872 <right_flank>ggggcctcac</right_flank>
873 </contributing_site>
874 <contributing_site sequence_id="sequence_8" position="13" strand="plus" pvalue="8.57e-04" >
875 <left_flank>TATAACTCAG</left_flank>
876 <site>
877 <letter_ref letter_id="G"/>
878 <letter_ref letter_id="T"/>
879 <letter_ref letter_id="T"/>
880 <letter_ref letter_id="G"/>
881 <letter_ref letter_id="G"/>
882 <letter_ref letter_id="A"/>
883 <letter_ref letter_id="T"/>
884 <letter_ref letter_id="A"/>
885 <letter_ref letter_id="A"/>
886 <letter_ref letter_id="A"/>
887 <letter_ref letter_id="A"/>
888 </site>
889 <right_flank>TAATTTGTAC</right_flank>
890 </contributing_site>
891 <contributing_site sequence_id="sequence_10" position="7" strand="plus" pvalue="1.47e-03" >
892 <left_flank>aaactta</left_flank>
893 <site>
894 <letter_ref letter_id="A"/>
895 <letter_ref letter_id="A"/>
896 <letter_ref letter_id="A"/>
897 <letter_ref letter_id="C"/>
898 <letter_ref letter_id="T"/>
899 <letter_ref letter_id="C"/>
900 <letter_ref letter_id="T"/>
901 <letter_ref letter_id="A"/>
902 <letter_ref letter_id="T"/>
903 <letter_ref letter_id="A"/>
904 <letter_ref letter_id="A"/>
905 </site>
906 <right_flank>acttaaaact</right_flank>
907 </contributing_site>
908 <contributing_site sequence_id="sequence_2" position="26" strand="plus" pvalue="2.64e-03" >
909 <left_flank>GGTGGGGGTG</left_flank>
910 <site>
911 <letter_ref letter_id="G"/>
912 <letter_ref letter_id="G"/>
913 <letter_ref letter_id="G"/>
914 <letter_ref letter_id="G"/>
915 <letter_ref letter_id="T"/>
916 <letter_ref letter_id="T"/>
917 <letter_ref letter_id="T"/>
918 <letter_ref letter_id="C"/>
919 <letter_ref letter_id="A"/>
920 <letter_ref letter_id="C"/>
921 <letter_ref letter_id="T"/>
922 </site>
923 <right_flank>GGTCCACTAT</right_flank>
924 </contributing_site>
925 </contributing_sites>
926 </motif>
927 </motifs>
928 <scanned_sites_summary p_thresh="0.0001">
929 <scanned_sites sequence_id="sequence_0" pvalue="5.63e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="39" pvalue="1.41e-05"/>
930 </scanned_sites>
931 <scanned_sites sequence_id="sequence_1" pvalue="1.57e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="27" pvalue="3.93e-05"/>
932 </scanned_sites>
933 <scanned_sites sequence_id="sequence_2" pvalue="1.00e-01" num_sites="0"></scanned_sites>
934 <scanned_sites sequence_id="sequence_3" pvalue="2.49e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="14" pvalue="6.24e-05"/>
935 </scanned_sites>
936 <scanned_sites sequence_id="sequence_4" pvalue="1.22e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="12" pvalue="3.04e-05"/>
937 </scanned_sites>
938 <scanned_sites sequence_id="sequence_5" pvalue="1.47e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="0" pvalue="3.67e-05"/>
939 </scanned_sites>
940 <scanned_sites sequence_id="sequence_6" pvalue="6.45e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="15" pvalue="1.61e-05"/>
941 </scanned_sites>
942 <scanned_sites sequence_id="sequence_7" pvalue="2.26e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="4" pvalue="5.65e-05"/>
943 </scanned_sites>
944 <scanned_sites sequence_id="sequence_8" pvalue="3.37e-02" num_sites="0"></scanned_sites>
945 <scanned_sites sequence_id="sequence_9" pvalue="1.95e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="13" pvalue="4.86e-06"/>
946 </scanned_sites>
947 <scanned_sites sequence_id="sequence_10" pvalue="5.73e-02" num_sites="0"></scanned_sites>
948 <scanned_sites sequence_id="sequence_11" pvalue="5.52e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="16" pvalue="1.38e-05"/>
949 </scanned_sites>
950 <scanned_sites sequence_id="sequence_12" pvalue="2.59e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="18" pvalue="6.48e-06"/>
951 </scanned_sites>
952 <scanned_sites sequence_id="sequence_13" pvalue="1.10e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="13" pvalue="2.74e-06"/>
953 </scanned_sites>
954 <scanned_sites sequence_id="sequence_14" pvalue="7.78e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="17" pvalue="1.95e-05"/>
955 </scanned_sites>
956 <scanned_sites sequence_id="sequence_15" pvalue="5.52e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="21" pvalue="1.38e-05"/>
957 </scanned_sites>
958 <scanned_sites sequence_id="sequence_16" pvalue="2.85e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="22" pvalue="7.15e-05"/>
959 </scanned_sites>
960 <scanned_sites sequence_id="sequence_17" pvalue="1.90e-02" num_sites="0"></scanned_sites>
961 <scanned_sites sequence_id="sequence_18" pvalue="8.63e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="37" pvalue="2.16e-05"/>
962 </scanned_sites>
963 <scanned_sites sequence_id="sequence_19" pvalue="1.95e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="9" pvalue="4.86e-06"/>
964 </scanned_sites>
965 <scanned_sites sequence_id="sequence_20" pvalue="2.59e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="4" pvalue="6.48e-06"/>
966 </scanned_sites>
967 <scanned_sites sequence_id="sequence_21" pvalue="1.95e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="7" pvalue="4.86e-06"/>
968 </scanned_sites>
969 <scanned_sites sequence_id="sequence_22" pvalue="7.78e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="2" pvalue="1.95e-05"/>
970 </scanned_sites>
971 <scanned_sites sequence_id="sequence_23" pvalue="8.89e-05" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="15" pvalue="2.22e-06"/>
972 </scanned_sites>
973 <scanned_sites sequence_id="sequence_24" pvalue="1.80e-05" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="12" pvalue="4.51e-07"/>
974 </scanned_sites>
975 <scanned_sites sequence_id="sequence_25" pvalue="1.95e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="36" pvalue="4.86e-06"/>
976 </scanned_sites>
977 <scanned_sites sequence_id="sequence_26" pvalue="5.54e-03" num_sites="0"></scanned_sites>
978 <scanned_sites sequence_id="sequence_27" pvalue="5.54e-03" num_sites="0"></scanned_sites>
979 <scanned_sites sequence_id="sequence_28" pvalue="2.59e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="32" pvalue="6.48e-06"/>
980 </scanned_sites>
981 <scanned_sites sequence_id="sequence_29" pvalue="1.22e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="30" pvalue="3.04e-05"/>
982 </scanned_sites>
983 </scanned_sites_summary>
984 </MEME>